An Isis flag flies in Iraq. There are concerns the jihadist group is seeking to set up a ‘distant caliphate’ in Indonesia.
Photograph: Marwan Ibrahim/AFP/Getty Images

The Australian attorney-general has “no doubt at all” that Islamic State is seeking to establish a “distant caliphate” in Indonesia, “either directly or through surrogates”.

In comments made to the Australian newspaper during high-level security meetings in Jakarta between Australian and Indonesian ministers and security officials, George Brandis said Isis “has identified Indonesia as a location of its ambitions”.

“Isis has ambitions to elevate its presence and level of activity in Indonesia, either directly or through surrogates,” he said.

“You’ve heard the expression the ‘distant caliphate’? Isis has a declared intention to establish caliphates beyond the Middle East, provincial caliphates in effect. It has identified Indonesia as a location of its ambitions.”

In further remarks he warned Australia and Indonesia were “very vulnerable” to terrorism, particularly “Isis-inspired terrorism”.

But Greg Fealey, an expert in Islamism and Indonesian politics from the Australian National University, said Isis was not the major Islamist risk in Indonesia, despite comprising the larger part of the approximately 300 foreign fighters who have left the country for the middle east.

“I’m a bit skeptical,” Fealey told Guardian Australia. “Most scholars looking at Isis in south-east Asia and particularly in Indonesia are not convinced that Isis has big plans for Indonesia.”

“We’ve not seen Isis sending fighters back to Indonesia or Malaysia to undertake terrorist operations ... Nor has there been a statement from IS [Isis] centrally, indicating they would seek to establish a caliphate in south-east Asia or Indonesia.”

He said the small number of foreign fighters who returned to Indonesia had fought with al-Qaeda affiliate Jabhat al-Nusra.

“They do come back, within a year, and they are not interested in terrorism but are interested in using those skills to build an Islamic state.”

A separate meeting between the defence and foreign ministers of the two countries was held in Sydney and resulted in the signing of a memorandum of understanding on terrorism, among other agreements.

Australian justice minister, Michael Keenan, said sharing intelligence and policing resources were how the two countries could “work together to counter the virulent and violent message that is put out by Isis in the Middle East, particularly over social media”.

Aside from foreign fighters, the two governments identified cyber-security as a future area of co-operation.

Face-to-face recruitment was still the main factor in prompting the decision to leave Indonesia for distant warzones.

The report recommended monitoring Indonesians’ internet use for extremist material, excluding convicted terrorists and prisoners from internet and mobile phone usage, and the training of intelligence and police officers in cyber-security techniques.

Also useful, the report noted, were “disillusioned returnees who have come back from Syria with stories of corruption, false promises and discrimination by Arabs who treat southeast Asians as second-class citizens”.

Fealey noted that while the Indonesian police are capable of monitoring internet and phone usage, Australia may be able to assist with more sophisticated online operations, like tracking the transfers of overseas funds.

Even so, according to Fealey co-operation between the two countries is so close that any further progress from agreements to fight terrorism is likely to be diplomatic rather than technical.

“Now that relations have gotten better there’s an element of wanting to ink deals like this, to drive home the point that we have a functional and mutually beneficial relationship,” Fealey said.

He added that Malcolm Turnbull’s prime ministership has brought “warmth to the relationship that’s never been there under Abbott”, and that the government could capitalise on this.

Australia’s ministers were indeed positive during the meetings about Indonesia, which Keenan described as “the world’s largest Muslim majority country, but still pluralist, still a vibrant democracy, and a very successful model that needs to be exported to the rest of the world”.

The statements from Brandis and Kennan follow three days of raids across Java to thwart plans for a suicide attack in the capital, Jakarta.

Nine arrests were made in the raids, which ended on Sunday. Chemicals, detonators and a black flag, reportedly “Isis-inspired”, were confiscated.

The attacks were planned against police targets, members and ex-members of the counter-terrorism squad Densus and Shia Muslims, Indonesia’s chief of national police, Badrodin Haiti, said on Monday.

Those arrested are former members of Jemaah Islamiyah, the group responsible for the 2002 bombings in Bali that killed over 200.